I think I'm being unclear in my original post. I don't want the child to receive the signal, nor am I using this alarm as a timeout to make sure the system call doesn't hang.
In the real code, a connection to MySQL is established via the DBI module. Then a wget command is issued that takes a long time. During that time, the database connection times out, and must send a signal to the parent. This causes $? and $! to be set. But in addition to those, the system('wget') call returns -1. I know the wget succeeds, because the file is completely downloaded. But since system() returns -1, it looks like the wget failed!
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